Patres et Filii
by aadarshinah
Summary: Atlantis is filled with all sorts of things the Ancients left behind. Some are more interesting than others. Sequel to "Custodia." Ancient!John rewrite of "38 Minutes" and "Before I Sleep". McShep preSlash


Patres et Filii

A Sequel to Pastor and Custodia

* * *

><p>"So, life-sucking bugs, life-sucking aliens – anything else you might've forgotten to mention to us about life the Pegasus galaxy, Major?" Rodney asks as they walk towards the transporters.<p>

John has just been released from the infirmary and, while he'd been pronounced both alive and damage free, he is clearly still in a lot of pain. But he insists that all he wants to do was go back to his quarters and sleep, that the _Iratus bugs_ were nowhere near as bad as the Wraith, and that he'd be the picture of health when he wakes up. "Lots, probably. Don't know how accurate any of it is, though."

"Why don't you just start and we can cross things off the list later?"

"There _is_ a database you could try looking in, you know."

"Yes, and you also failed to index it, which I must say is a huge lack of foresight on your part. It really makes me wonder how you ever managed to develop Stargates and flying cities in the first place if you couldn't manage to tabulate your data in any useful way."

"You do realize that I am not personally responsible for all the failings of my race, don't you?"

"Yes, yes, of course I do."

"Besides, the Council had the index deleted when they returned to Terra."

"Earth," he corrects, "and why would they do something like that?"

"We named it first," John teases tiredly – or, at least, Rodney assumes he teases. As best as he can tell, John doesn't actually _care_ what names they use for anything. He's also been picking up Earth terms and colloquialisms as if by osmosis, almost making it seem as if he's trying his best to make them forget that he's not human, not from Earth, and was born at about the time most of the Expedition's ancestors were just starting to figure out farming.

In fact, John's said remarkably little about his people in the month or so they've been here. It's almost as if he's _ashamed_ that the Ancients – Alterans, Lanteans, Ancestors, take your pick – were so much more advanced than pretty much everyone else in the universe. Which is ridiculous, because Rodney's worked with more than a few Asgard in his time and suffice to say people with that amount of technological superiority didn't usually have a word for _humble_ in their language. Except, of course, the Ancients had been more advanced than even the Asgard. They'd _built the Stargates_ for crying out loud. And intergalactic spaceships the size of Manhattan. And basically seeded life in their image throughout two galaxies, if not more.

Maybe that was the problem: the fact that Rodney's ancestors were pretty much the lab mice of John's. That is bound to be uncomfortable, if you care about such things.

"Yes, but we live there, so squatter's rights and all." And that's when he notices hallway beyond is dark, smelling of dust and mould and mildew, and most definitely _not_ one of the areas of the city they've been able to explore yet. "Where the hell are we?"

For a moment, John looks just as confused as Rodney feels, before, "Sorry, I must be more tired than I thought."

Ah. "Your old quarters were down here, weren't they?"

His, "No," surprises Rodney. "My father's are, though."

For a moment Rodney wonders what it must be like to have a parent you would want to go see after a day like this. "Oh. Well, you want to check it out anyway?"

The Major pauses, hand poised over the panel that will take them back to the inhabited parts of the city. If he'd looked tired before, he appears positively haggard now, as if all the years he'd spent in stasis were finally catching up with him. "Nothing's likely to have survived."

"Still, worth a look, right? And you said something about him keeping a list of all the ZedPMs. Maybe we could find a copy of it in there."

"Maybe later..." John hedges, but then lights start flickering on up and down the hall, though both are still firmly inside the transporter. Frowning, "'Lantis," he says, glancing at the ceiling in the way he does when speaking to the city, "what are you doing?"

Rodney, of course, doesn't hear the response. _That_ honour is seemingly only bestowed on John, and he'll admit that for a full seventy-eight minutes he was jealous, but then an article had magically appeared on one of his tablets, drawn from the Ancient database and appended to a note that read:

**We Do Like You**

in much the same way he'd been alerted to John's existence when they'd first arrived here.

The article had talked of the Ancients building their great city-ships with complex virtual intelligences, to aid them in crossing the great voids between galaxies back when their technology was far less advanced when it was now, during a time called The _Schisma _that none of his queries will reveal anything further about. It had also talked about them keying their technology to a gene they'd engineered into their genome, and how, somehow, the two together had had unintended consequences – that, after their city-ships became self-aware, they began responding to specific gene-users differently than others. The ones they favoured were called _custodiae_. The ones that went and put millions of microscopic machines in their head were _pastores, _and they were the most beloved at all.

Since there was no way in hell _that_ was happening (he _knows_ it's different, but he's read one too many files on the Replicatiors to ever seriously consider it, thank you very much), Rodney's decided it's more than enough to hear Atlantis' song like an unending sympathy in the back of his mind. She's the most amazing thing he's ever heard, and some nights he's lain in bed just listening to her, grateful and ashamed by turns that he gave up the piano so long ago – grateful, because there's no way he could ever hope to capture anything more than the barest glimmer of the wonder that is Atlantis; ashamed, because it seems wrong that no one else can hear her music.

Besides, ever since his gene therapy took, John's developed this tendency to talk aloud to the city. He doesn't do it all the time, and, when he does, it's always when they're alone, but it helps.

"She says she's not the one doing it."

"Well that's crazy. If it's not her, who? There's no one else here. We're not scheduled to check out this part of the city for- Where _are_ we anyway?" John tells him. "Well, definitely not us then. We're not scheduled to head this way for a couple weeks, at least."

"It's not the city either – something on it's own separate circuit." With a long-suffering sigh, he adds, "It's coming from Father's quarters," and, with that, he heads down the hall, opening a door midway down it's length.

What they find he doesn't even think John expects.

Or maybe he does, because he takes one look at the glowing figure standing in the middle of the room and immediately goes to the nearest couch, collapsing into it in a way that suggests this is one hundred percent normal for the Pegasus galaxy, so why not get it over with and see what the man wants?

"It's only an _eminentia,_" John says after a moment, not looking at the slowly rotating figure. "A projection of light and sound."

"A hologram. Of course there's a hologram in your living room. You have transporters, so why not holograms?" At this point, he'd hardly be surprised to find out that Gene Roddenberry had run across an Ancient shortly before conceiving _Star Trek_. A much more helpful and scientifically-inclined Ancient than John. "This your father, I take it? There is some family resemblance, at least, though I'm surprised to see he doesn't have your hair. That from your mother's side, I presume? He does seem to have your smirk though – yes, that one you're giving me now."

John continues smirking, though it seems a bit forced. "Yeah, that's Father."

"Cool." He watches the hologram of John's dad rotate back and forth for a couple of minutes before being compelled to ask, "You going to see what he wants?"

"I suppose I should. 'Lantis?" he glances up at the ceiling, the way he always does when talking to the city, "Any way you can download my translation matrix into the _eminentia_? Thanks," he adds, tapping his radio. "Elizabeta? Can you come down section 12? McKay and I have found something you'll probably want to see."

Rodney turns away from the hologram and his thoughts on how to adapt the tech into his own holodeck to stare at the major. "Why'd you ask Elizabeth to come down here?"

"'Cause she probably will want to see this."

"Yes, strangely enough I got that part. What I mean is, it's a hologram of your father. Don't you want to, I dunno, listen to it in private?"

John's face darkens. "It's not likely to be that kind of message, Rodney."

He doesn't know what to say to that, so he collapses into the seat next to him and makes a show of pulling up a program to record this on his tablet.

"No matter. Elizabeta says she's in the middle of something and I'm half-asleep already, so what do you say we just go ahead and get this over with."

"Major?" he asks, trying to fit whole questions – _why would your father leave something like this behind _and _why is it coming on now_ and _if your relationship with him was that bad, why did you come here in the first place_ – into one word. He's no idea if he's successful, but if the yawn John gives as he leans across him to activate the message is any indication, the Major doesn't have the energy to sit up straight at the moment, let alone to answer any question more complicated than _are you asleep_?

The projection of John's father stops spinning, instead glancing about the room before catching sight of them sitting on his couch, his son – or the son of the man who'd made the projection – leaning heavily against Rodney's shoulder.

The man in the hologram is dressed much like he expects all Ancients to dress, which is to say in various shades of white with highly visible, highly impractical laces down the back, and heavy cloth vambraces that couldn't possibly serve any practical purpose. (The anthropologists have made much of this, as well as the fact that, after John managed to acquire an Expedition uniform of his own, he's continued to wear one of his Ancient bracers. Seeing John evade their questions on the subject is a work of artifice and misdirection he's not seen since his last visit to the Pentagon.) And, while he doesn't have John's hair, the eyes are the same and say far more than the raised eyebrow that accompanies his announcement, "Licinus. You're looking terrible."

"Had a run-in with an Iratus bug off-world. There was some delay in removing it."

Rodney can't help but snorting at this, because, really, _understatement, thy name is John Sheppard_, or Licinus, or whatever the hell John wanted to call himself. Either way, the noise draws the hologram's attention, and it's eyes sharpened perceptively, as if in warning, though warning what to whom, he couldn't say. "Who's your friend, Licinus?"

"Doctor Rodney McKay," he answers for himself. "of Earth. Head of the Science and Research Departments, such as they are, on this Expedition. "

The word _science_ seems to mollify the hologram somewhat, for he reciprocates: "Ianus Ishachidus Ianitos Rector, Lantean Director of Science... and Licinus' father, or, rather, my counterpart was, before the Exodus. How long has it been by the way?"

"Just over ten thousand years."

"Really?" the hologram asks, Rodney all but forgotten. But that's okay, because he's trying to process _John's father was, quite possibly, the basis for the Roman god Janus_, which, admittedly, isn't that much of a deal after working for the SGC for the last seven years. It's more of the _the lab John told me about was the Director of Science's lab _and _John's father was the Director of Science_, which, somehow, is more shock-inducing. "The _cathedra_ kept you in stasis that long? You barely look like you've aged at all."

"Seemed to last no longer than a dream," John agrees, "but you didn't build an _eminentia _to ask me about the long-term effects of _cathedra _stasis. At least, not only, so why all the games with the lights and such?"

"To get your attention, mostly, and to make sure the right person got this message. I knew that if the Wraith ever breeched the defences, you'd try to destroy Atlantis, but I couldn't know if you'd be successful and didn't want the information in this program accessible to just anyone..."

"You can say what you want in front of McKay. I trust him."

"Hmm. Where is this _Earth_ anyway?"

"It's Terra – you know how descendants are about naming things. A couple of them actually have the gene needed to use our tech. I wouldn't be surprised if they're some of your personal descendants. So, you see, they're practically family. Now what about this message?"

The hologram actually looks abashed for the moment, mumbling, "Oh. Well. Yes," and very much not denying the accusations. Which, while moderately disturbing, probably explains some of John's awkwardness when it comes to talking about his life before the Expedition found him. It continues, "I assumed you'd come down here eventually and wanted to make sure you'd be able to survive if you woke from the _cathedra_ to find yourself alone – my program contains a list of outposts the Council sent additional _potentia _before the Exodus, as well as a handful of those we hid among our Pegasus descendants. I've also included some designs for what _servola_ you can probably fabricate from the materials we left behind, though I doubt they'll be of much good to you until you solve your energy problem... Don't even bother trying to repair the secondary power systems – they'll never be able to power any significant part of Atlantis and, without a live _potentia_, you'll not be able to store the energy in any useful manner...

"Once in Avalon, it was my intention to seek out the Furlings as soon as it was possible to do so without alerting the Council. It was my hope that, with their help, I would be able to find a path that would lead those who remained back to Atlantis, possibly even with a way to defeat the Wraith... but, since it has been so long, I can only assume I failed."

"You don't know that. The Terrans found us, didn't they?"

Janus' hologram sighs. "Perhaps..." There is silence for a beat. "I know why you stayed. Given the chance, I would have done the same. But... I wish things had worked out differently with us."

It's impossible for Rodney to read the expression on John's face. Normally he'd be the first to admit people are his weak point, but that has nothing to do with it this time. This look, it's so intense Rodney's not sure he's ever seen it before on anyone. There might be something in German for the emotion – they tend to have words for the complicated emotions that English lacks, - but Rodney wouldn't put money on it. John's, "Me too," is partly filled with familial affection, partly with filial annoyance, and mixed with more than a little melancholy, contempt, and frustration for good measure, but even knowing this Rodney doesn't think he's captured the emotion properly.

It's quiet, too quiet, after that. The only sound he can hear Atlantis' faint _berceuse, _and even that's only a whisper in the back of his mind. It's only when John's head dips forward further that he realises the other man has finally lost his battle with exhaustion. He'd laugh, only he doesn't want to wake him, so he settles for rolling his eyes at Janus' hologram and easing John off his shoulder.

When he looks up again, it's to the unbounded remorse in the hologram's eyes. Janus' face quickly shutters, wiping away all hints of emotion, but not quickly enough.

Rodney swallows uncomfortably. "I'll just..."

"Is that device of yours," the hologram interrupts, "capable of interfacing with Lantean equipment?"

"Yes. Of course. Why?"

"I programmed this _eminentia_ to erase itself two hours after activation. It would be best that you download the planetary addresses and _servola _schematics before then. My flesh-and-blood counterpart would have hated to go through all this trouble for nothing to come of it in the end."

"Ah." He doesn't know whether to be appalled by the paranoia or to applaud it. Either way, he pushes himself off the couch and gets to work, opening a panel on the small pyramidal device on the table that seems to be the hologram projector.

It's not silence that follows, but it's close and goes on for long enough that Rodney actually thinks his tampering with the projector has caused Janus' hologram to disappear entirely.

He's just pressed the download button when Janus speaks again, shocking him enough that he nearly drops his tablet. "You're a _custodia_, aren't you Doctor Rodney McKay?"

"Er, yes?" That's what John called him, anyway, and John would know better than anyone. _He_ still didn't quite believe it.

"Then you know he's lying."

That stops Rodney cold. He knows that John's been keeping things from them – about the war, the Ancients, himself – but outright lying? That doesn't seem to be John's style. He's only known him a month, but Rodney would be willing to bet his life on that. He's already done so. The whole Expedition has.

But still, he has to ask: "About what?"

"Not remembering. Ten thousand years in a _cathedra_, in constant communication with an _urbs-navis_ with more sensors and scanners and systems most our descendants can dare imagine might one day exist? Even if Licinus doesn't consciously realise it, he's bound to remember every moment of it, in excruciating detail."

"How do you know?" _You're just a hologram_, he doesn't add. Just like Atlantis isn't just a city. They might not be on the same level, but there's a level of intelligence to both, even if it's only the illusion thereof. And, even if it's true, it's not like it's an _important _lie. "Seen many causes of ten-thousand-year stasis, have you?"

The look Janus flashes him is the same one John gives the anthropologists when they ask something stupid. "No. But it's changed him. I can tell."

"You can tell?"

"We talked."

"And?" he gestures for him to go on.

"We didn't yell."

"What?"

"We talked for a good ten, fifteen minutes and neither of us raised our voices once. The last time I think that happened, he was still a small boy... The solitude must have been crippling."

Blinking, he asked (rather intelligently in his opinion given the way this conversation was progressing), "What?" once more.

But Janus' response was, "Someone comes this way," followed by his hologram blinking out of existence for ever and ever more.

The _someone_ turns out to be Elizabeth, who looks over the scene – Rodney kneeling by the table with the hologram projector, John dead asleep on the white, water-stained couch slightly off to the side – and manages to minimize her response to an amused smirk. "Major Sheppard said there was something he wanted me to see?"

Rodney stands, because, really, his knees are going to _kill_ him for that later, and rolls his eyes at her. But Janus' words echo in his mind, even after he fills her in on the relevant details and they head back to the control room to start deciphering the information they've been given.

He should be excited. There are _twenty_ addresses that might lead them to zero point modules on the list. And, as if that weren't enough, _designs for servola_ apparently translated to _schematics for robots_, specifically, robots that could help them repair the more inaccessible parts of the city. He _is_ excited. The whole science department is.

And if Rodney takes a moment during his very important and exciting research to take a blanket down to John, well, that's what friends do. Crippling hypothermia is the last thing anyone needs after having the life sucked out of them by an overgrown bug.

And if he takes more moments ever few hours to check up on him, well, that's just what friends do too.

* * *

><p><strong>an: **I seem to keep hacking away at my larger sequel to "Pastor" - this was supposed to be part 1 of 3, but, once again, I decided the "Underground"/"The Storm"/"The Eye" retelling would stand better on its own, without this bit. Which, in case you hadn't noticed, is supposed to take place after "38 Minutes" - though it also serves as this 'verse's "Before I Sleep". Will be posted on lj once the ddos attacks stop.

* * *

><p>Relevant translations:<p>

_Patres et Filii_ - Fathers and Sons; also the title of a book by Ivan Turgenv

_Schisma_ - Schism, in this case refering to the Alteran/Ori split

_Pastor_ - Iohannes' title, translates to _shepherd_

_Custodia_ - can be considered Rodney's title, translates to _guardian_

_Eminentia _- Hologram

_Rector_ - Janus' title, roughly equivolent to the Dean of a College

_Cathedra_ - Control Chair

_Potentia_ - ZPM

_Servola_ - litterally means "small slaves;" in this case, means _robots_

_Urbs-Navis_ - City-Ship

_Berceuse_ - French loanword, a kind of lullaby


End file.
